2HYE

Crystal Structure of the DDB1-Cul4A-Rbx1-SV5V Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.253 

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This is version 1.3 of the entry. See complete history


Literature

Molecular architecture and assembly of the DDB1-CUL4A ubiquitin ligase machinery.

Angers, S.Li, T.Yi, X.MacCoss, M.J.Moon, R.T.Zheng, N.

(2006) Nature 443: 590-593

  • DOI: 10.1038/nature05175
  • Primary Citation of Related Structures:  
    2HYE

  • PubMed Abstract: 
  • Protein ubiquitination is a common form of post-translational modification that regulates a broad spectrum of protein substrates in diverse cellular pathways. Through a three-enzyme (E1-E2-E3) cascade, the attachment of ubiquitin to proteins is catalysed by the E3 ubiquitin ligase, which is best represented by the superfamily of the cullin-RING complexes ...

    Protein ubiquitination is a common form of post-translational modification that regulates a broad spectrum of protein substrates in diverse cellular pathways. Through a three-enzyme (E1-E2-E3) cascade, the attachment of ubiquitin to proteins is catalysed by the E3 ubiquitin ligase, which is best represented by the superfamily of the cullin-RING complexes. Conserved from yeast to human, the DDB1-CUL4-ROC1 complex is a recently identified cullin-RING ubiquitin ligase, which regulates DNA repair, DNA replication and transcription, and can also be subverted by pathogenic viruses to benefit viral infection. Lacking a canonical SKP1-like cullin adaptor and a defined substrate recruitment module, how the DDB1-CUL4-ROC1 E3 apparatus is assembled for ubiquitinating various substrates remains unclear. Here we present crystallographic analyses of the virally hijacked form of the human DDB1-CUL4A-ROC1 machinery, which show that DDB1 uses one beta-propeller domain for cullin scaffold binding and a variably attached separate double-beta-propeller fold for substrate presentation. Through tandem-affinity purification of human DDB1 and CUL4A complexes followed by mass spectrometry analysis, we then identify a novel family of WD40-repeat proteins, which directly bind to the double-propeller fold of DDB1 and serve as the substrate-recruiting module of the E3. Together, our structural and proteomic results reveal the structural mechanisms and molecular logic underlying the assembly and versatility of a new family of cullin-RING E3 complexes.


    Organizational Affiliation

    Howard Hughes Medical Institute, University of Washington, School of Medicine, Box 357280, Seattle, Washington 98195, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA damage-binding protein 1A1140Homo sapiensMutation(s): 0 
Gene Names: DDB1XAP1
Find proteins for Q16531 (Homo sapiens)
Explore Q16531 
Go to UniProtKB:  Q16531
NIH Common Fund Data Resources
PHAROS:  Q16531
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nonstructural protein VB222Mammalian orthorubulavirus 5Mutation(s): 0 
Gene Names: P/V
Find proteins for P11207 (Parainfluenza virus 5 (strain W3))
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Go to UniProtKB:  P11207
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cullin-4AC759Homo sapiensMutation(s): 0 
Gene Names: CUL4A
Find proteins for Q13619 (Homo sapiens)
Explore Q13619 
Go to UniProtKB:  Q13619
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PHAROS:  Q13619
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
RING-box protein 1D108Homo sapiensMutation(s): 0 
Gene Names: RBX1RNF75ROC1
EC: 2.3.2.27 (UniProt), 2.3.2.32 (UniProt)
Find proteins for P62877 (Homo sapiens)
Explore P62877 
Go to UniProtKB:  P62877
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PHAROS:  P62877
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.253 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.452α = 90
b = 203.165β = 90
c = 424.875γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-03
    Type: Initial release
  • Version 1.1: 2007-10-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description